tsRFun

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tsRTarget

tsRTarget: Identify tsRNAs-target interactions from CLIP-Seq and CLASH data

Parameters Selection

01 Select Sequencing Data Type

CLEAR / CLASH

iCLIP / eCLIP / PAR-CLIP / HITS-CLIP
02 Select Reads Aligment Parameters

Number of Allowed mismatch:

Shortest tsRNA Length (nt):

Shortest Target Length (nt):

Collapse PCR duplicates:
03 Select Target Prediction Parameters (Seed Region)

Start of Seed Region (nt):

End of Seed Region (nt):

MFE:
04 Select Target Prediction Parameters (non-Seed Region)

Match Length (nt):

Gap Open:
05 Select miRNA Target Prediction Parameters

Number of Allowed mismatch:

Shortest tsRNA Length (nt):

Shortest Target Length (nt):

Start of Seed Region (nt):

End of Seed Region (nt):

MFE:

Collapse PCR duplicates:

Match Length (nt):

Gap Open:

File Selection

Paste sequences

Paste small RNA sequences in FASTQ format or FASTA format into the text area below.
Note: For FASTA data, the identical reads must be collapsed together. The header format is >A_B_xC, A indicate the name of the sample, B is the id of the sequence, C is the total count of the sequence.

Example-result

Or upload your FASTA file

Note: High volume files in FASTA format (200 MB file size limit for our server). For time-saving, we recommend the users to upload compressed file in Zip, tar.gz or RAR format.

Example Files: zip tar.gz rar fasta